Mercurial > repos > jackcurragh > ribogalaxy_umi_extraction
comparison UMI_riboseq_tool/UMI_riboseq.xml @ 0:393b73b2eb5f draft
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| author | jackcurragh |
|---|---|
| date | Mon, 25 Jul 2022 12:22:53 +0000 |
| parents | |
| children | 4605a1af1f3d |
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| -1:000000000000 | 0:393b73b2eb5f |
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| 1 <tool id="UMI_riboseq" name="UMIs to Header" version="0.1.8"> | |
| 2 <requirements> | |
| 3 <requirement type="package" version="1.75">biopython</requirement> | |
| 4 </requirements> | |
| 5 <command detect_errors="exit_code"> | |
| 6 <![CDATA[ python3 '$__tool_directory__/UMI.py' $reads $output $gzip $five_prime_UMI_length $three_prime_UMI_length]]> | |
| 7 </command> | |
| 8 <inputs> | |
| 9 <param format="fastqsanger,fastqsanger.gz" name="reads" type="data" label="fastqsanger,fastqsanger.gz"/> | |
| 10 <param name="gzip" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Gzip the outputted FASTQ" /> | |
| 11 <param name="five_prime_UMI_length" type="integer" value=2 label="Number of UMI bases at the 5' end" help="2 for McGlincy Ingolia Protocol" /> | |
| 12 <param name="three_prime_UMI_length" type="integer" value=5 label="Number of UMI bases at the 3' end)" help="5 for McGlincy Ingolia Protocol" /> | |
| 13 | |
| 14 </inputs> | |
| 15 <outputs> | |
| 16 <data format="fastqsanger" name="output"/> | |
| 17 </outputs> | |
| 18 <tests> | |
| 19 <test> | |
| 20 <param name="reads" value="sub_10k_reads.fq.gz"/> | |
| 21 <output name="output" file="output"/> | |
| 22 </test> | |
| 23 <test> | |
| 24 <param name="reads" value="sub_10k_reads2.fq"/> | |
| 25 <output name="output" file="output2"/> | |
| 26 </test> | |
| 27 </tests> | |
| 28 <help> | |
| 29 <![CDATA[ fastq/fastq.gz are input files with reads containing UMIs (already demultiplexed and adapters are removed). | |
| 30 The output of the script is fastq/fastq.gz file where UMIs (7nt in total, 5'NN and 3'NNNNN preceding barcode consisting of 5nt) are in header of the read. It is designed for protocol: McGlincy NJ, Ingolia NT. Transcriptome-wide measurement of translation by ribosome profiling. Methods. 2017;126:112-129. doi:10.1016/j.ymeth.2017.05.028 ]]> | |
| 31 </help> | |
| 32 <citations> | |
| 33 <citation type="bibtex"> @misc{FedorovaAD2022, author = {Fedorova Alla}, year = {2022}, title = {UMI_for_riboseq}, publisher = {GitHub}, journal = {GitHub repository}, url = {https://github.com/triasteran/RiboGalaxy_with_ansible/blob/main/toolshed_tools/UMI_riboseq_tool/UMI.py}, } | |
| 34 </citation> | |
| 35 </citations> | |
| 36 </tool> |